DUF4926 - PFAM28P - GREMLIN Contacts

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DUF4926 - Domain of unknown function (DUF4926)

PFAM:	PF16277	Sequences: ELDVVALTRDLPEHGLRRGDVGTVVEVYAPGEAYEVEFVDADGRTYAVVTLPASQLRV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	58 (57)
Sequences:	10657 (6047)
Seq/√Len:	801.0
META:	0.963

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
9_R	55_Q	3.388	1.00
28_Y	35_E	2.514	1.00
1_E	26_E	2.399	1.00
52_P	55_Q	2.276	1.00
17_R	20_D	2.085	1.00
10_D	18_R	2.041	1.00
35_E	50_T	1.967	1.00
7_L	16_L	1.889	1.00
10_D	17_R	1.887	1.00
14_H	49_V	1.845	1.00
34_Y	53_A	1.750	1.00
40_D	44_R	1.744	1.00
2_L	26_E	1.708	1.00
4_V	23_T	1.643	1.00
6_A	21_V	1.607	1.00
6_A	57_R	1.547	1.00
8_T	18_R	1.501	1.00
29_A	33_A	1.276	1.00
45_T	48_V	1.266	1.00
11_L	55_Q	1.265	1.00
28_Y	33_A	1.250	1.00
20_D	46_Y	1.238	1.00
39_V	45_T	1.205	1.00
26_E	35_E	1.194	1.00
11_L	14_H	1.134	1.00
27_V	34_Y	1.083	1.00
7_L	38_F	1.021	1.00
40_D	46_Y	1.014	1.00
51_L	55_Q	1.008	1.00
22_G	36_V	1.005	1.00
34_Y	56_L	0.998	1.00
27_V	32_E	0.963	1.00
28_Y	48_V	0.945	1.00
29_A	32_E	0.942	1.00
32_E	53_A	0.915	1.00
23_T	39_V	0.895	1.00
22_G	38_F	0.868	1.00
38_F	47_A	0.857	1.00
8_T	57_R	0.853	1.00
24_V	34_Y	0.822	1.00
36_V	56_L	0.821	1.00
5_V	56_L	0.819	1.00
30_P	33_A	0.803	1.00
4_V	39_V	0.801	1.00
25_V	37_E	0.757	1.00
51_L	56_L	0.753	1.00
33_A	50_T	0.750	1.00
31_G	53_A	0.728	1.00
14_H	47_A	0.726	1.00
41_A	46_Y	0.723	1.00
7_L	51_L	0.705	1.00
39_V	48_V	0.703	1.00
11_L	51_L	0.698	1.00
4_V	21_V	0.670	1.00
2_L	23_T	0.647	1.00
27_V	30_P	0.641	1.00
33_A	53_A	0.614	1.00
35_E	49_V	0.612	1.00
20_D	57_R	0.603	1.00
11_L	15_G	0.602	1.00
39_V	46_Y	0.596	1.00
3_D	34_Y	0.578	1.00
1_E	27_V	0.578	1.00
16_L	47_A	0.574	1.00
46_Y	57_R	0.573	1.00
33_A	52_P	0.573	1.00
37_E	48_V	0.571	1.00
5_V	22_G	0.567	1.00
53_A	56_L	0.560	1.00
28_Y	50_T	0.550	1.00
37_E	45_T	0.546	1.00
5_V	36_V	0.544	1.00
16_L	38_F	0.539	1.00
39_V	44_R	0.533	1.00
24_V	36_V	0.527	1.00
21_V	41_A	0.522	1.00
11_L	16_L	0.520	1.00
32_E	52_P	0.520	1.00
2_L	24_V	0.514	1.00
40_D	43_G	0.513	1.00
20_D	43_G	0.511	1.00
1_E	28_Y	0.504	1.00
12_P	16_L	0.501	1.00
27_V	31_G	0.500	1.00
25_V	45_T	0.500	1.00
31_G	52_P	0.500	1.00

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
2y35A	1	0.8103	64.1	0.761	Contact Map
3pieA	1	0.931	54.2	0.774	Contact Map
1w36D	1	0.1207	35.6	0.798	Contact Map
4l0jA	2	0.8966	21.3	0.819	Contact Map
3e1sA	1	0.8621	13.6	0.835	Contact Map
4hczA	1	0.7931	12.9	0.836	Contact Map
2ldmA	1	0.8103	11	0.841	Contact Map
3p8dA	2	0.8103	10.9	0.842	Contact Map
2eyqA	1	0.931	10.4	0.843	Contact Map
4fibA	1	0.9483	10.4	0.843	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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